Since NCBI change a policy (HTTP to HTTPS) in using SRA data, HISAT2 was updated to version 2.0.5. I have HISAT2 2.0.1 installed with homebrew.

I want to update it to the latest version downloaded from the site (source code) and want to add NCBI-NGS support (to work directly with SRA files).
According to the instructions I should use make with next options

"make USE_SRA=1 NCBI_NGS_DIR=/path/to/NCBI-NGS-directory NCBI_VDB_DIR=/path/to/NCBI-NGS-directory, where NCBI_NGS_DIR and NCBI_VDB_DIR will be used in Makefile for -I and -L compilation options.
For example, $(NCBI_NGS_DIR)/include and $(NCBI_NGS_DIR)/lib64 will be used."

However, when I checked the ngs directory in /usr/local/ I found that directory /include and /lib64 located under /usr/local/ngs/ngs-sdk

I have two questions.
1. If I install the HISAT2 from the source, what will happen to simlinks from homebrew installation?
2. Should I use actual path to the directory /include and /lib64 or I can use the path to directory /ngs ?
Thank you